The following paragraph (no. 163), from page 39, of the Ordnance Instructions for the Confederate States Navy (almost certainly also relating to similar circumstances in the Union Navy, and included in their own Instructions), answers at least one of your questions:

"The call for 'Firemen' to repair to the spar deck will be given verbally and by strking the ship's bell rapidly. The rapid ringing of the bell will be the FIRE ALARM at all times, when the crew will immediately assemble at quarters."

I have not yet had time to check other Navy instructions, in my collections, for further data on these subjects.

Also, an examination of photographs of vessels from the Civil War years, does show steam exhaust pipes (whistles?) on at least some of these vessels. See especially my own web site titled PHOTO ESSAY 3: USS AGAWAM OR USS MACKINAW? at http://home.ozconnect.net/tfoen/photoessay3.htm